When the car goes into water, the best thing you can do for yourself is to stay calm. Your instinct is for flight, obviously, but getting yourself worked up is not going to do you any good. You have to think clearly. Going into the deep-end (sorry, had to) will most likely cause your demise.
Proactively, you need to know your car. It's strange, but even when submerged in water, the electrics will still have a chance to work. They won't short out automatically, so use them to roll the window down ... or at least try. You aren't hurting anything by doing so.
If that doesn't work, you'll most likely need to bust a window out. Don't even try to bust the front window out (at least for US cars), as this is laminated glass (glass/laminate/glass), which is very tough stuff. You'll wear yourself out in most cases before you'll break it out. The side windows are going to be your best bet, but you must get a stress riser formed, or you'll not get anywhere. Someone else mentioned using a headrest post ... this is an awesome idea, but you still have to hit the window hard enough for it to shatter. The back window is safety glass as well, but it is going to be much harder to get to than will the side windows.
Speaking of the back window, if you can get there on a car with a hatch, you can most likely get it to pop. The back end of the vehicle is usually the last to go down, as the engine will tip it forward. If you can pop the back hatch through the use of a manual popping mechanism, this will lead you to safety as well. It will also ensure the car doesn't take you down with it as you'll be escaping the back as it's going forward.